title: glioblastoma_HD_337


title: Human Bronchial Epithelium exposed to 15% oxygen rep3

status: Public on Oct 31 2019

type: RNA

city: Oklahoma City

first: david

middle: c

last: hutchings

state: OK

address: 6500 S MacArthur Blvd

department: CAMI

country: USA

institute: FAA

description: Gene expression data from bronchial epithelial cells harvested after treatment at 15% oxygen for 16 hours

hyb_protocol: 5.5 ug of fragmented and labeled ss-cDNA was hybridized onto Affymetrix Genechip HTA 2.0 arrays using the GeneChip Hybridization, Wash, and Stain Kit (16h, 60 RPM, 45 C).

scan_protocol: Affymetrix FS450-0001 using an Affymetrix 7G GeneChip scanner

data_processing: Data was analysed in Affymetrix Transcriptome Analysis Console.  Normalization was conducted using the RMA-SST wethod, detection threshold was: 50 % of samples are expressed above background (DAGB p < 0.05) and AUC > 0.7.  Differential expression thershold set at FDR <= 0.05.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human brochial epithelial cells after 16 h at 15% oxygen.

label_protocol: 100 ng of RNA was amplified to ss-cDNA, of which 5.5 ug was fragmented and labeled using the Affymetrix GeneChip WT PLUS Reagent kit.

growth_protocol: Cells were grown under standard conditions (5% CO2, 37 C, 100% humidity) for three passages in Lonza Bronchial Epithelial Growth Medium.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit on a QiaCube automation platform.

treatment_protocol: At the fourth passage, 100,000 cells each were aliquotted into individual wells of a 6-well plate, grown under standard conditions for 24 hours, then treated for 16 hours under 21%, 15%, or 2% oxygen.  Cells were harvested and placed into 250 uL Qiazol, then frozen at -80C.

tag: tissue

value: Human Bronchial Epithelium

tag: gender

value: male

tag: treatment

value: 15 percent oxygen


title: Human Bronchial Epithelium exposed to 21% oxygen rep1

description: Gene expression data from bronchial epithelial cells harvested after treatment at 21% oxygen for 16 hours

source_name: Human brochial epithelial cells after 16 h at 21% oxygen.

value: 21 percent oxygen


title: Human Bronchial Epithelium exposed to 15% oxygen rep2


title: Human Bronchial Epithelium exposed to 2% oxygen rep3

description: Gene expression data from bronchial epithelial cells harvested after treatment at 2% oxygen for 16 hours

source_name: Human brochial epithelial cells after 16 h at 2% oxygen.

value: 2 percent oxygen


title: Human Bronchial Epithelium exposed to 2% oxygen rep2


title: glioblastoma_HD_336

type: genomic

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

hyb_protocol: bisulphite conerted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC/450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2.
Average Beta normalized with a BMIQ method.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: glioblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

value: glioblastoma

tag: sample preparation

value: female


title: glioblastoma_HD_354


title: WT RNA-seq 1

type: SRA

city: Beijing

first: Xu

last: Wang

address: No. 12 Zhongguancun south road

country: China

institute: Institute of crop sciences, CAAS

description: transcriptome profiling of WT (wild type)

library_source: transcriptomic

data_processing:
The paired end reads were aligned to genome sequences using TopHat (Trapnell et al., 2009) allowing up to two mismatches. Splice junction sequences required at least four bases on each side of the junction. Reads mapped to multiple locations as well as only uniquely mapped reads were used and compared with each other to avoid the improper deletion of reads for subsequent analysis.
Genome_build: Arabidopisis
Supplementary_files_format_and_content: wig files were generated using MACS program

organism: Arabidopsis thaliana

source_name: 12-day-old Col-0 seedlings grown in long days

growth_protocol: In the method of plant cell paper

extract_protocol:
Total RNAs were extracted from 12-day-old seedlings of wild type (WT), M1 (nup96-1) and M2 (hos1-3)
RNA-seq dUTP protocal

treatment_protocol: No treatment

value: seedlings

tag: age

tag: genotype/variation

value: wild type


title: IPSC_Endoderm_8Day_0001uMRetinoicAcid_sample42

city: Research Triangle Park

first: Thomas

last: Knudsen

state: NC

address: 109 T.W. Alexander Drive (D-143-02)

department: NCCT/ORD

institute: US EPA

data_processing:
Raw sequence data in FASTQ format were assessed for quality (FastQC) and ribosomal RNA content (sortmeRNA)
Reads were aligned to the human genome (GRCh38) with Ensemble (v84) gene annotations using HISAT2 (version 2.0.5) default parameters, with the exception of the “downstream transcript assembly” flag. The index for the Ensemble reference genome was created using HISAT2 build and the corresponding FASTA files obtained from Ensembl. Multiple alignments per read were allowed, but only uniquely aligned reads were used in downstream analysis.
HTSeq v0.9.0 was used to count uniquely mapped reads for each gene ID in Ensembl (v84) with parameters: stranded = no, intersection = nonempty.
For each gene with row median counts > 5, the fold change compared to time-matched DMSO control (treatment / control) was calculated for each sample using DESeq2 (v1.15.3).
Counts were then filtered to select differentially expressed genes with padj value < 0.05 (Benjamini-Hochberg adjustment method) and absolute value of log2(fold change) >1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-separated values (csv) files were generated using Htseq. These files include unfiltered read counts for each gene.

extract_protocol:
Pelleted cells were snap frozen, then total RNA was extracted using the mirVana miRNA Isolation kit, with phenol (Ambion/ThermoFisher) according to manufacturer's protocol.
Species specific rRNA-probes were hybridized to total RNA to remove nuclear-encoded and mitochondrial contaminating ribosomal RNA from the sample. The resulting ribo-depleted RNA was then fragmented. First-strand cDNA synthesis was performed using reverse transcriptase and random primers in the presence of Actinomycin D, followed by second-strand cDNA synthesis with DNA polymerase I and RNase H. Double-stranded cDNA was end-repaired and A-tailed for subsequent adaptor ligation. Indexed adaptors were ligated to the A-tailed cDNA. Enrichment by PCR was performed to generate the final cDNA sequencing library. Libraries were sequenced at a read depth of at least 30 million single-end 75 base pair reads on an Illumina NextSeq500 (San Diego, CA) following the manufacturer's protocols.

tag: cell type

value: iPSCs from adult female fibroblasts

tag: cell subtype

value: differentiating endoderm from hiPSC

tag: atra concentration (µm)

tag: timepoint


title: Human Bronchial Epithelium exposed to 15% oxygen rep1


title: glioblastoma_HD_335


title: glioblastoma_HD_334


title: M1 RNA-seq 3

description: transcriptome profiling of M1

source_name: 12-day-old nup96-1 seedlings grown in long days


title: IPSC_Endoderm_8Day_001uMRetinoicAcid_sample40


title: IPSC_Endoderm_8Day_001uMRetinoicAcid_sample39


title: IPSC_Endoderm_8Day_01uMRetinoicAcid_sample38


title: IPSC_Endoderm_8Day_01uMRetinoicAcid_sample37


title: IPSC_Endoderm_8Day_1uMRetinoicAcid_sample36


title: glioblastoma_HD_332


title: IPSC_Endoderm_8Day_0001uMRetinoicAcid_sample41


title: glioblastoma_HD_347


title: IPSC_Endoderm_8Day_10uMRetinoicAcid_sample33


title: WT RNA-seq 2


title: IPSC_Endoderm_8Day_10uMRetinoicAcid_sample34


title: IPSC_Endoderm_8Day_1uMRetinoicAcid_sample35


title: glioblastoma_HD_331


title: glioblastoma_HD_348


title: IPSC_Endoderm_8Day_Undifferentiated_sample32

value: undifferentiated hiPSC


title: glioblastoma_HD_349


title: glioblastoma_HD_330


title: glioblastoma_HD_329


title: Human Bronchial Epithelium exposed to 2% oxygen rep1


title: glioblastoma_HD_333


title: IPSC_Endoderm_8Day_Undifferentiated_sample31


title: IPSC_Endoderm_8Day_01%DMSO_sample30


title: glioblastoma_HD_328


title: IPSC_Endoderm_6HR_0001uMRetinoicAcid_sample27


title: Human Bronchial Epithelium exposed to 21% oxygen rep2


title: IPSC_Endoderm_6HR_001uMRetinoicAcid_sample26


title: glioblastoma_HD_327


title: IPSC_Endoderm_6HR_001uMRetinoicAcid_sample25


title: glioblastoma_HD_326


title: glioblastoma_HD_325


title: IPSC_Endoderm_6HR_01uMRetinoicAcid_sample23


title: IPSC_Endoderm_6HR_01uMRetinoicAcid_sample24


title: IPSC_Endoderm_6HR_10uMRetinoicAcid_sample20


title: IPSC_Endoderm_6HR_1uMRetinoicAcid_sample21


title: IPSC_Endoderm_6HR_1uMRetinoicAcid_sample22


title: glioblastoma_HD_324


title: IPSC_Endoderm_6HR_Undifferentiated_sample18


title: IPSC_Endoderm_8Day_01%DMSO_sample29


title: IPSC_Endoderm_6HR_10uMRetinoicAcid_sample19


title: glioblastoma_HD_322


title: IPSC_Endoderm_6HR_01%DMSO_sample15


title: IPSC_Endoderm_6HR_01%DMSO_sample16


title: IPSC_Endoderm_4Day_0001uMRetinoicAcid_sample14


title: glioblastoma_HD_321


title: IPSC_Endoderm_4Day_0001uMRetinoicAcid_sample13


title: IPSC_Endoderm_4Day_001uMRetinoicAcid_sample12


title: glioblastoma_HD_320


title: IPSC_Endoderm_4Day_001uMRetinoicAcid_sample11


title: IPSC_Endoderm_4Day_01uMRetinoicAcid_sample9


title: glioblastoma_HD_319


title: IPSC_Endoderm_4Day_01uMRetinoicAcid_sample10


title: glioblastoma_HD_318


title: IPSC_Endoderm_4Day_1uMRetinoicAcid_sample7


title: IPSC_Endoderm_4Day_1uMRetinoicAcid_sample8


title: IPSC_Endoderm_4Day_10uMRetinoicAcid_sample6


title: glioblastoma_HD_317


title: IPSC_Endoderm_4Day_10uMRetinoicAcid_sample5


title: IPSC_Endoderm_6HR_Undifferentiated_sample17


title: glioblastoma_HD_316


title: IPSC_Endoderm_4Day_Undifferentiated_sample4


title: glioblastoma_HD_323


title: IPSC_Endoderm_4Day_Undifferentiated_sample3


title: IPSC_Endoderm_4Day_01%DMSO_sample2


title: IPSC_Endoderm_4Day_01%DMSO_sample1


title: glioblastoma_HD_315


title: glioblastoma_HD_314


title: sgRNA-enrichment_5K-sgRNAs_Batch_5_2

city: Dallas

first: Gary

last: Hon

state: TX

address: 5323 Harry Hines Blvd, J7.125, Hon Lab

institute: UT Southwestern Medical Center

description:
RX227
Single-cell RNA-Seq

data_processing:
custom pipeline
Mapping and library combination were performed by using 10X Cellranger V2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: summary of UMI count of each sgRNA for every cell barcode

source_name: K562 cells

growth_protocol: K562 were cultured in IMDM plus 10% FBS and pen/strep at 37C and 5% CO2.

extract_protocol:
Cells were collected, washed once with PBS. Then the cells were resuspended in PBS containing 0.05% BSA to the desired concentration and immediately load on the 10X Chromium controller for the single-cell RNA-seq preparation.
For single-cell library preparation, we follow the standard protocol of 10X Chromium 3’ V2 kit. After the cDNA amplification, 20µg of samples were separated for the sgRNA enrichment library preparation.

treatment_protocol: A lentivirus library containing 5170 sgRNAs was constructed and packaged by transfecting HEK293T cells. The virus was collected 72 hours after transfection and concentrated by using Lenti-X lentivirus concentrator. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection. Each batch represents one individual experiment starting from virus packaging. We performed two 10X runs for each batch. To acquire a better sgRNA coverage for each cell, a sgRNA enrichment PCR was performed after cDNA amplification of each 10X library to build the sgRNA enrichment library.

tag: cell line

value: K562 cells

tag: experiment

value: Single-cell Expression, sgRNA enrichment

tag: batch


title: sgRNA-enrichment_5K-sgRNAs_Batch_3_1

description:
RX218
Single-cell RNA-Seq


title: sgRNA-enrichment_5K-sgRNAs_Batch_3_2

description:
RX219
Single-cell RNA-Seq


title: glioblastoma_HD_313


title: glioblastoma_HD_312


title: sgRNA-enrichment_5K-sgRNAs_Batch_1_2

description:
RX199
Single-cell RNA-Seq


title: sgRNA-enrichment_5K-sgRNAs_Batch_5_1

description:
RX226
Single-cell RNA-Seq


title: sgRNA-enrichment_5K-sgRNAs_Batch_1_1

description:
RX198
Single-cell RNA-Seq


title: sgRNA-enrichment_5K-sgRNAs_Batch_2_1

description:
RX214
Single-cell RNA-Seq


title: glioblastoma_HD_311


title: sgRNA-enrichment_5K-sgRNAs_Batch_2_2

description:
RX215
Single-cell RNA-Seq


title: glioblastoma_HD_310


title: sgRNA-enrichment_5K-sgRNAs_Batch_4_2

description:
DAA45
Single-cell RNA-Seq


title: glioblastoma_HD_309


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-5_2

description:
RX225
Single-cell RNA-Seq

data_processing:
Basecalls performed 10X Cellranger V2.1.0
Mapping and library combination were performed by using 10X Cellranger V2.1.0
Genome_build: hg38
Supplementary_files_format_and_content: sample matrix in hdf5 format

treatment_protocol: A lentivirus library containing 5170 sgRNAs was constructed and packaged by transfecting HEK293T cells. The virus was collected 72 hours after transfection and concentrated by using Lenti-X lentivirus concentrator. For virus infection, 2X105 K562 cells were seeded in 24 well plate per well with 500 µl complete medium plus 1µg/ml polybrene. The plate was then centrifuged at 1000xg at 36 °C and returned to the incubator. The following day, the media was changed to fresh complete medium with antibiotics to screen for infected cells. Cells were kept at ~30% confluence during antibiotic selection. Each batch represents one individual experiment starting from virus packaging. We performed two 10X runs for each batch.

value: Single-cell Expression


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-5_1

description:
RX224
Single-cell RNA-Seq


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-2_2

description:
RX213
Single-cell RNA-Seq


title: glioblastoma_HD_308


title: glioblastoma_HD_307


title: sgRNA-enrichment_5K-sgRNAs_Batch_4_1

description:
DAA44
Single-cell RNA-Seq


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-2_1

description:
RX212
Single-cell RNA-Seq


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-3_2

description:
RX217
Single-cell RNA-Seq


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-1_2

description:
RX197
Single-cell RNA-Seq


title: glioblastoma_HD_306


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-1_1

description:
RX196
Single-cell RNA-Seq


title: glioblastoma_HD_304


title: glioblastoma_HD_302


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-4_2

description:
DAA43
Single-cell RNA-Seq


title: glioblastoma_HD_305


title: glioblastoma_HD_300


title: glioblastoma_HD_299


title: glioblastoma_HD_296


title: glioblastoma_HD_295


title: glioblastoma_HD_298


title: glioblastoma_HD_291


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-3_1

description:
RX216
Single-cell RNA-Seq


title: glioblastoma_HD_290


title: glioblastoma_HD_288


title: glioblastoma_HD_284


title: glioblastoma_HD_283


title: K562-dCas9-KRAB_5K-sgRNAs_Batch-4_1

description:
DAA42
Single-cell RNA-Seq


title: glioblastoma_HD_294


title: glioblastoma_HD_281


title: glioblastoma_HD_280


title: glioblastoma_HD_253


title: glioblastoma_HD_301


title: glioblastoma_HD_297


title: brain_malignantglioma_NOA-08_093

description:
tumor
This sample failed quality control. No processed data available.

data_processing: BeadStudio software v3.2. Average Beta values normalized with a BMIQ method.

source_name: malignant glioma

extract_protocol: Genomic DNA was extracted and pruified from FFPE tissue according with the Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

tag: who grade


title: glioblastoma_HD_292


title: glioblastoma_HD_293


title: glioblastoma_HD_289


title: glioblastoma_HD_287


title: glioblastoma_HD_286


title: IPSC_Endoderm_6HR_0001uMRetinoicAcid_sample28


title: brain_malignantglioma_NOA-08_100

description: tumor


title: brain_malignantglioma_NOA-08_097

description: tumor


title: glioblastoma_HD_303


title: brain_malignantglioma_NOA-08_096

description: tumor


title: brain_malignantglioma_NOA-08_104

description: tumor


title: brain_malignantglioma_NOA-08_089

description: tumor

value: anaplastic astrocytoma


title: brain_malignantglioma_NOA-08_082

description: tumor


title: brain_malignantglioma_NOA-08_088

description: tumor


title: brain_malignantglioma_NOA-08_102

description: tumor


title: brain_malignantglioma_NOA-08_086

description: tumor


title: brain_malignantglioma_NOA-08_085

description: tumor


title: brain_malignantglioma_NOA-08_094

description: tumor


title: brain_malignantglioma_NOA-08_103

description: tumor


title: brain_malignantglioma_NOA-08_078

description: tumor


title: brain_malignantglioma_NOA-08_087

description: tumor


title: brain_malignantglioma_NOA-08_071

description: tumor


title: brain_malignantglioma_NOA-08_099

description: tumor


title: brain_malignantglioma_NOA-08_090

description: tumor


title: brain_malignantglioma_NOA-08_074

description: tumor


title: brain_malignantglioma_NOA-08_083

description: tumor


title: brain_malignantglioma_NOA-08_084

description: tumor


title: brain_malignantglioma_NOA-08_072

description: tumor


title: brain_malignantglioma_NOA-08_076

description: tumor


title: brain_malignantglioma_NOA-08_075

description: tumor


title: brain_malignantglioma_NOA-08_079

description: tumor


title: brain_malignantglioma_NOA-08_073

description: tumor


title: brain_malignantglioma_NOA-08_081

description: tumor


title: brain_malignantglioma_NOA-08_101

description: tumor


title: brain_malignantglioma_NOA-08_070

description: tumor


title: brain_malignantglioma_NOA-08_069

description: tumor


title: brain_malignantglioma_NOA-08_068

description: tumor


title: brain_malignantglioma_NOA-08_067

description: tumor


title: brain_malignantglioma_NOA-08_080

description: tumor


title: brain_malignantglioma_NOA-08_058

description: tumor


title: brain_malignantglioma_NOA-08_066

description: tumor


title: brain_malignantglioma_NOA-08_054

description: tumor


title: brain_malignantglioma_NOA-08_056

description: tumor


title: brain_malignantglioma_NOA-08_064

description: tumor


title: brain_malignantglioma_NOA-08_052

description: tumor


title: brain_malignantglioma_NOA-08_044

description: tumor


title: brain_malignantglioma_NOA-08_060

description: tumor


title: brain_malignantglioma_NOA-08_048

description: tumor


title: brain_malignantglioma_NOA-08_034

description: tumor


title: brain_malignantglioma_NOA-08_062

description: tumor


title: brain_malignantglioma_NOA-08_043

description: tumor


title: brain_malignantglioma_NOA-08_050

description: tumor


title: brain_malignantglioma_NOA-08_038

description: tumor


title: brain_malignantglioma_NOA-08_045

description: tumor


title: brain_malignantglioma_NOA-08_046

description: tumor


title: brain_malignantglioma_NOA-08_051

description: tumor


title: brain_malignantglioma_NOA-08_055

description: tumor


title: brain_malignantglioma_NOA-08_042

description: tumor


title: brain_malignantglioma_NOA-08_041

description: tumor


title: brain_malignantglioma_NOA-08_033

description: tumor


title: brain_malignantglioma_NOA-08_049

description: tumor


title: brain_malignantglioma_NOA-08_037

description: tumor


title: brain_malignantglioma_NOA-08_032

description: tumor


title: 3h_Plus_Triptolide_1

city: new york

first: Danny

last: Reinberg

state: new york

address: 522 first avenue

department: Biochemistry

institute: NYU school of Medicine

description: 3h release into S-phase, 1uM treatment of Triptolide

data_processing:
Quality of sequencing was assessed with FastQC v0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads having less than 80% of quality scores above 25 were removed with NGSQCToolkit v2.3.3
Reads were aligned to the mouse mm10 reference genome from Illumina igenomes UCSC collection using bowtie v1.0.0 allowing 3 mismatches and keeping uniquely aligned reads
Sam ouputs were converted to Bam with Samtools v1.0.6
Data were further processed with Pasha v0.99.21 with the following parameters: WIGvs = TRUE, incrArtefactThrEvery = 7000000, elongationSize = NA.
Fixed steps wiggle files were converted to bigwigs with the script wigToBigWig available on the UCSC Genome Browser website (http://hgdownload.soe.ucsc.edu/admin/exe/)
The wiggle files of 50 bp bins were converted to 200 bp bins with an in-house script
Spike-in normalization was achieved using Drosophila Melanogaster DNA aligned to Illumina igenomes dm3
Genome_build: mm10 and dm3
Supplementary_files_format_and_content: Fastq files for raw data, bigwigs of the processed and spike-in normalized experiments are provided.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: KH2 mESCs were grown in DMEM supplemented with 15% FBS (for CRISPR/Cas9 targeting) or Tet-free FBS (Gemini 100-800, for biotinylation experiments), L-glutamine, penicillin/streptomycin, non-essential amino acids, 0.1 mM β-mercaptoethanol, LIF, and 2i inhibitors which includes 1 µM MEK1/2 inhibitor (PD0325901) and 3 µM GSK3 inhibitor (CHIR99021).

extract_protocol:
For native MNase chromatin preparation, nuclei were harvested from mESCs by hypotonic lysis TMSD buffer (40 mM Tris, 5 mM MgCl2, 0.25 M Sucrose with protease inhibitors), pelleted for 10 min at 3600 rpm at 4° C. Nuclei were solubilized by resuspending in NIB-250 (15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 250 mM Sucrose with protease inhibitors) containing 0.3% NP-40. A chromosome pellet was isolated by centrifuging the solubilized nuclei for 5 min at 600 rcf at 4° C. The chromosome pellet was washed with NIB-250 buffer, then resuspended with MNase digestion buffer (10 mM Hepes, 50 mM NaCl, 5 mM MgCl2, 5 mM CaCl2 with protease inhibitors) and treated with MNase (Sigma) until a DNA fragment size of 150-500 bp (1-3 nucleosomes) was attained. MNase digestion was stopped with 15 µl of EGTA (0.5 M) per 1 ml pellet and then spun at 600 rcf for 5 min at 4° C. The supernatant was placed in a fresh tube and the chromatin pellet was further processed by adding the same volume of BC500 (40 mM Tris, 5 mM MgCl2, 500 mM NaCl and 5% glycerol, and protease inhibitors) and EGTA (0.5 M) as in the MNase buffer plus EGTA step. The soluble chromosomes in BC500 and EGTA were then incubated for 30 min while rotating at 4° C, allowing for further enrichment of desired chromatin. Samples were pelleted at 600 rcf and the BC500 supernatant was pooled with an equal volume of MNase-treated supernatant to acquire the starting chromatin material for chromatin immunoprecipitations (IPs).
For ChIP-seq, libraries were prepared by standard protocol. First, fragments are repaired to generate  blunt 5' P ends  using 'EndIT DNA End Repair kit' (Epicentre). Second, 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB). Third,  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Lastly, libraries were size selected using 'Ampure beads' (Beckman Coulter), then amplified, quantified and pooled. For RNA-seq, polyA-beads were used to purify mRNA followed by cDNA synthesis prior to standard library constructions as described above.

treatment_protocol: For G1 synchronization experiments, mESCs were plated at 50-60% confluency and pulsed for 18 hr with 8 µM Thymidine, followed by a PBS wash and a 7-8 hr release into 2i Tet-free media. mESCs were then given a second Thymidine treatment at a 5-6 µM concentration for 12-13 hr. For the biotinylation experiments, a 6 hr pulse of 2 µg/ml of doxycycline and 1µg/ml of exogenous biotin was given during the latter half of the second Thymidine treatment and cells were harvested at the G1/S-block (time 0h) or through one DNA replication (time 12h). For Retinoic Acid (RA) samples, 1uM of RA was added before double Thymidine synchronization.

value: Embryonic Stem Cell

tag: genotype

value: KH2:13 Flag-BAP-H3 tags


title: brain_malignantglioma_NOA-08_047

description: tumor


title: 6h_No_Triptolide_1

description: 6h release into S-phase, no treatment with Triptolide


title: 3h_No_Triptolide_1

description: 3h release into S-phase, no treatment with Triptolide


title: Quadriceps

first: Adwait Amod

last: Sathe

state: Texas

address: 5323 Harry Hines Blvd.

department: McDermott Center of Human Growth and Development

data_processing:
BCL files were demultiplexed using cellranger(v3.0.0)
Alignment, barcode counting, UMI counting were performed using cellranger(v3.0.0)
PCA, clustering, and differential expression was performed using Seurat
Genome_build: mm10
Supplementary_files_format_and_content: count matrix in a sparse matrix format
Supplementary_files_format_and_content: barcode id of the sample
Supplementary_files_format_and_content: gene ids of the sample

source_name: Cells isolated from limb muscle (quadriceps)

extract_protocol: Quadriceps and diaphragm were collected from C57BL/6J mice. To minimize the individual variability, 10 mice were used for the experiment. Each tissue was minced in 2.5 ml digestion solution (1 U/ml collagenase B and 1 U/ml dispase II (Roche Diagnostics, Indianapolis, IN, USA) in PBS) and incubated at 37ºC for 1 hour. The reaction was terminated by adding 10 ml PBS containing 10% fetal bovine serum (FBS). The mixture was then filtered through a 70-mm cell strainer and centrifuged at 250 g for 5 minutes. The pellet was collected and the supernatant was centrifuged again at 250 g for 5 minutes. The pellet was combined with the pellet from the first centrifugation, washed with PBS, and centrifuged at 670 g for 10 minutes. The pellet was re-suspended in 3 ml PBS and filtered through a 40-mm cell strainer. For brain, cell suspension was layered on equal volume of 50% isotonic Percoll (Sigma-Aldrich) and centrifuged at 600 g for 25 minutes. Supernatant was then discarded and cell pellet was re-suspended in FACS staining buffer.The cell suspension was layered on equal volume of the Lympholyte-M solution (Cedarlane, Burlington, NC, USA) and centrifuged at 2,095 g for 45 minutes. Cells at the interface were collected, centrifuged at 670 g for 10 minutes, and re-suspended in FACS staining buffer. Cells from multiple quadriceps or diaphragm were combined, respectively. Viable cells were then sorted by flow cytometry based on FSC/SSC.

value: limb muscle (quadriceps)

tag: strain


title: brain_malignantglioma_NOA-08_065

description: tumor


title: Gata6_RA_Input

description: G1/S-block cells treated with Retinoic Acid (RA)

library_source: genomic

tag: chip-antibody

value: none (input)


title: Gata6_RA_IgG_Dox_12h

description: Cells with BirA targeting to Gata6 locus treated with Retinoic Acid (RA)

tag: tissue

value: IgG


title: brain_malignantglioma_NOA-08_031

description: tumor


title: Diaphragm

source_name: Cells isolated from respiratory muscle (diaphragm)

value: respiratory muscle (diaphragm)


title: brain_malignantglioma_NOA-08_023

description: tumor

value: glioblastoma


title: H3K27me3_Input

description: G1/S-block cells

source_name: G1/S-block cells


title: H3K27me3

description: G1/S-block cells


title: Gata6_RA_IgG_Dox_0h

description: G1/S-block cells with BirA targeting to Gata6 locus treated with Retinoic Acid (RA)


title: Gata6_RA_IgG_No_Dox

source_name: G1/S-block cells treated with Retinoic Acid (RA)


title: brain_malignantglioma_NOA-08_018

description: tumor


title: HoxC_minusDox_0h_flag

description: G1/S-block cells

value: Flag


title: brain_malignantglioma_NOA-08_026

description: tumor


title: brain_malignantglioma_NOA-08_024

description: tumor


title: Gata6_RA_Biotin_Dox_12h

source_name: Cells with BirA targeting to Gata6 locus treated with Retinoic Acid (RA)

value: Biotin


title: brain_malignantglioma_NOA-08_025

description: tumor


title: 6h_Plus_Triptolide_1

description: 6h release into S-phase, 1uM treatment of Triptolide


title: Gata6_RA_Biotin_Dox_0h

source_name: G1/S-block cells with BirA targeting to Gata6 locus treated with Retinoic Acid (RA)


title: HoxC_minusDox_0h

description: G1/S-block cells


title: brain_malignantglioma_NOA-08_020

description: tumor


title: Gata6_RA_Biotin_No_Dox


title: brain_malignantglioma_NOA-08_017

description: tumor


title: HoxC_input

description: G1/S-block cells


title: HoxC_plusDox_0h

description: G1/S-block cells with BirA targeting to Hoxc6 locus


title: Gata6_2i_IgG_Dox_12h

description: Cells with BirA targeting to Gata6 locus


title: brain_malignantglioma_NOA-08_077

description: tumor


title: EBF1_Biotin_Plus_Dox

description: G1/S-block cells with BirA targeting to Ebf1 locus


title: brain_malignantglioma_NOA-08_016

description: tumor


title: brain_malignantglioma_NOA-08_015

description: tumor


title: Gata6_2i_IgG_No_Dox

description: G1/S-block cells


title: brain_malignantglioma_NOA-08_011

description: tumor


title: Gata6_2i_IgG_Dox_0h

description: G1/S-block cells with BirA targeting to Gata6 locus


title: EBF1_input

description: G1/S-block cells


title: brain_malignantglioma_NOA-08_013

description: tumor


title: EBF1_Biotin_No_Dox

description: G1/S-block cells


title: Gata6_2i_Biotin_Dox_12h

source_name: Cells with BirA targeting to Gata6 locus


title: brain_malignantglioma_NOA-08_030

description: tumor


title: brain_malignantglioma_NOA-08_012

description: tumor


title: Gata6_2i_Biotin_Dox_0h

source_name: G1/S-block cells with BirA targeting to Gata6 locus


title: Gata6_2i_Input

description: G1/S-block cells


title: brain_malignantglioma_NOA-08_009

description: tumor


title: Gata6_2i_Biotin_No_Dox

description: G1/S-block cells


title: Y_B7_rep3

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

description:
Dev-B7-3
processed data file: TPM_matrix.txt

data_processing:
Adaptor sequences were removed, and the reads were de-multiplexed using the bcl2fastq v. 2 software (Illumina).
Gene expression values were quantified using Kallisto v. 0.42.4 with the options: --bias -b 100 -t 31 --single -l 350 -s 50 (Bray et al., 2016).
Genome_build: Amino acid and coding sequences and annotation for R. varieornatus were downloaded from www.ensembl.tardigrades.org (Hashimoto et al., 2016; Yoshida et al., 2017).
Supplementary_files_format_and_content: *.abundance.tsv: Output of Kallisto 0.44.0; Tab-delimited text file.
Supplementary_files_format_and_content: TPM_matrix.txt: Tab-delimited text file includes TPM values.

organism: Ramazzottius varieornatus

source_name: Whole body

growth_protocol: R. varieornatus was maintained using the methods previously described (Horikawa et al., 2008). Briefly, individuals were placed on 2% Bacto agar (Difco) gels prepared with Volvic water and fed with Chlorella vulgaris (Chlorella Industry). Individuals were moved to a new plate every week. The cultures were examined on a daily basis to obtain eggs and were observed every day to obtain juvenile samples for days 2-7.

extract_protocol:
Specimens were thoroughly washed with Milli-Q water on a sterile nylon mesh (Millipore), and were placed in a low-binding PCR tube. Pipette tips were used to homogenize the animals and lysed with the TRIzol reagent (Life Technologies). Total RNA was extracted using a Direct-zol RNA kit (Zymo Research), and the quality was validated with High Sensitivity RNA ScreenTape on TapeStation 2200 (Agilent Technologies).
The mRNA was amplified with the SMARTer Ultra Low Input RNA Kit for Sequencing v.3, and Illumina libraries were prepared with the KAPA HyperPlus Kit (KAPA Biosystems). The library was quantified using the Qubit Fluorometer (Life Technologies), and size distribution was validated with TapeStation D1000 ScreenTape (Agilent Technologies). The library was size-selected for 200 bp by manually cutting out an agarose gel and was purified with a NucleoSpin Gel and PCR Clean-up kit (Clontech).

value: Day 7 of juvenile stage

value: Whole body


title: Y_B7_rep2

description:
Dev-B7-2
processed data file: TPM_matrix.txt


title: Y_B7_rep1

description:
Dev-B7-1
processed data file: TPM_matrix.txt


title: Y_B6_rep3

description:
Dev-B6-3
processed data file: TPM_matrix.txt

value: Day 6 of juvenile stage


title: brain_malignantglioma_NOA-08_008

description: tumor


title: brain_malignantglioma_NOA-08_014

description: tumor


title: brain_malignantglioma_NOA-08_029

description: tumor


title: Y_B5_rep3

description:
Dev-B5-3
processed data file: TPM_matrix.txt

value: Day 5 of juvenile stage


title: Y_B6_rep2

description:
Dev-B6-2
processed data file: TPM_matrix.txt


title: brain_malignantglioma_NOA-08_027

description: tumor


title: brain_malignantglioma_NOA-08_028

description: tumor


title: Y_B5_rep1

description:
Dev-B5-1
processed data file: TPM_matrix.txt


title: Y_B5_rep2

description:
Dev-B5-2
processed data file: TPM_matrix.txt


title: primary CD4+T lymphocytes very slow, M7

first: Zhisheng

last: Jiang

state: Beijing

address: No.5 Yiheyuan Road

department: Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences

institute: Peking University

description: T-cells Male M7

data_processing:
Quantification of transcript abundances from bulk RNASeq data. Software: kallisto. Version: 0.42.3
Supplementary_files_format_and_content: Processed files are h5 files with the abundance of each gene in the sample in TPM (transcripts per million) and .tsv files with est_count and tpm

source_name: blood of healthy human donors, ficoll-histopaque gradient, CD4 Microbeads Kit

growth_protocol:
cultured for 15 days in the presence of the cytokines IL-7 and IL-15 to allow the cells undergo homeostatic proliferation
Mouse embryonic fibroblasts (MEFs) were routinally maintained in DMEM supplemented with 10% serum (LifeTech), HEPES (ThermoFisher), Sodium Pyrivate (ThermoFisher), non-essential amminoacids (ThermoFisher), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol(ThermoFisher).
Mouse embryonic stem cell line (EL16.7) was routinally maintained in 2i/LIF medium contains a 1:1 mixture of  DMEM/F12 supplemented with N2 (LifeTech) and neurobasal media (LifeTech) supplemented with glutamine (LifeTech), B27 (LifeTech), insulin (Sigma), 1x penicillin-streptomycin (PanBiotech), 2-mercaptoethanol (ThermoFisher), LIF (Orfgenetics), PD0325901(Sigma)  and CHIR9021 (Deltaclon).

extract_protocol: Total RNA was extracted from each sample with the Maxwell RNA Purification Kit (Promega) according to manufacturer's instructions

treatment_protocol:
Cells were stained with 10uM CFSE for 20min at 37C and sorted after 24h
Cells were stained with 10uM CFSE for 20min at 37C. The day after they were stained with Hoechst (LifeTech) and 50nM TMRE was added to the cell culture media for 20 minutes at 37 ̊C.

value: blood

value: primary CD4+T lymphocytes

tag: facs bin

value: P9 very slow


title: Y_B4_rep3

description:
Dev-B4-3
processed data file: TPM_matrix.txt

value: Day 4 of juvenile stage


title: primary CD4+T lymphocytes slow, M5

description: T-cells Male M5

value: P7 slow


title: Y_B4_rep2

description:
Dev-B4-2
processed data file: TPM_matrix.txt


title: brain_malignantglioma_NOA-08_010

description: tumor

value: anaplastic astrocytoma


title: primary CD4+T lymphocytes fast, M1

description: T-cells Male M1

value: P3 fast


title: brain_malignantglioma_NOA-08_007

description: tumor


title: Y_B4_rep1

description:
Dev-B4-1
processed data file: TPM_matrix.txt


title: primary CD4+T lymphocytes medium, M3

description: T-cells Male M3

value: P5 med


title: primary CD4+T lymphocytes very slow, F7

description: T-cells Female F7


title: brain_malignantglioma_NOA-08_003

description: tumor


title: Y_B3_rep3

description:
Dev-B3-3
processed data file: TPM_matrix.txt

value: Day 3 of juvenile stage


title: primary CD4+T lymphocytes slow, F5

description: T-cells Female F5


title: Y_B3_rep2

description:
Dev-B3-2
processed data file: TPM_matrix.txt


title: primary CD4+T lymphocytes medium, F3

description: T-cells Female F3


title: primary CD4+T lymphocytes fast, F1

description: T-cells Female F1


title: brain_malignantglioma_NOA-08_005

description: tumor


title: Y_B3_rep1

description:
Dev-B3-1
processed data file: TPM_matrix.txt


title: Y_B2_rep3

description:
Dev-B2-3
processed data file: TPM_matrix.txt

value: Day 2 of juvenile stage


title: Y_B2_rep2

description:
Dev-B2-2
processed data file: TPM_matrix.txt


title: A16_low-dose antibiotics

city: Shenzhen

first: Yihe

middle: Anya

last: ZHANG

address: No. 7, Pengfei Road

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

description: strand-special mRNA sequencing approach for library contructions

data_processing:
Basecalls performed using CASAVA
DNA reads are trimmed by cutadapt and masked for low-complexity or low-quality sequence then mapped to Sscrofa11.1 using software bsmap version 2.73 with parameters -v 6 -g 2 -p 8 -x 500 -m 0 -R -u -n 1
Methylation Ratio are calculated using methratio.py from software bsmap with parameters -t 2 -u -n -z -q -i correct
RNA reads are removed adaptor sequences and low quality sequences using software SOAPnuke version 1.0.1 with parameters by default aligned to the genome scrofa11.1 using Tophat2 version 2.0.12  with default parameters
Fragments per kilobase of exon per million fragments mapped (FPKM) are caculated using the Cufflinks version 2.2.1 following the default options and added the -G/--GTF guide
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Cout files include methylaion ratio and fpkm files were generated using Cufflinks

organism: Sus scrofa

source_name: Liver

growth_protocol: 32 piglets in LDA group were fed with low-dose antibiotics at age of 21±2 days and feedings were continuous for 4 weeks.

extract_protocol:
For RNA-seq:RNAs were extracted by Trizol and quantified by Qubit®3.0 fluorometer (Thermo fisher scientific, Cat#Q33216). A total amount of 1.5 μg RNA per liver sample was used as input material for preparations. For Bisulfite-seq:DNAs of liver tissues from these piglet samples were extracted by DNeasy Blood & Tissue Kits (QIAGEN, Cat#69504) according to the manufactural instruments and quantified by Qubit®3.0 fluorometer (Thermo fisher scientific, Cat#Q33216).
For RNA-seq:Sequencing libraries were constructed using NEBNext® UltraTM RNA library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. In brief, mRNA was purified from the total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH). Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNaseH, with the dUTP instead of deoxythymidine triphosphate (dTTP). Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR, which allowed selective degradation of the second cDNA strand contained dUTP for the reservation of the transcript direction and strand-specific information. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq4000 PE Cluster Kit (Illumina) according to the manufacturer’s instructions. For Bisulfite-seq: Briefly, 1 μg DNA of per sample was processed by fragmentation using Covaris, following with blunt end repair, 3′-adenylation, and 5′-methylcytosine index adapter ligation. Then, 250 ng DNA from each of three/four adapter-ligated libraries were pooled together for the liquid hybridization capture procedure. The hybridization probe was synthesized and purchased from Roche Nimblegen Incorporation. Finally, the captured DNA was eluted in 50 μl of 10 M NaOH with incubation at room temperature for 10 min. The supernatant was transferred into a new tube and neutralized with 50 μl of 10 M HAc and then purified using MiniElute PCR Purification Kit (QIAGEN, Cat#28004). For bisulfite conversion, 200 ng of unmethylated λDNA was added into each captured product and then ZYMO EZ DNA Methylation-Gold Kit™ (ZYMO, Cat#D5005) was employed to convert unmethylated cytosine into uracil according to the instructions. After purification, PCR was carried out with JumpStart™ Taq DNA Polymerase (Sigma, Cat#D9307) using the program of 94°C 30s, 15 cycles of 94°C 10 s, 60°C 30 s, 72°C 40s then prolong at 72°C for 5 min and hold at 12°C. The PCR products were purified using AMPure XP beads (Agencourt, Cat#A63881) and were quantified by the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).

treatment_protocol: 32 female DLY (Duroc×Landrace×Yorkshire) piglets were supplied by Sichuan Agricultural University. Antibiotics were mixed in the fodder according to government standards (Chlortetracycline was mixed with the concentration of 75 g/t, and virginiamycin was 25 g/t), half of which were LDA group and the other half were control (CON) group.

tag: breed

value: Duroc x Landrace x Yorkshire

tag: developmental stage

value: piglet

value: liver

tag: Sex

value: female

tag: treatment

value: low-dose antibiotics


title: A15_low-dose antibiotics


title: brain_malignantglioma_NOA-08_001

description: tumor

value: glioblastoma


title: A14_low-dose antibiotics


title: brain_malignantglioma_NOA-08_006

description: tumor


title: A13_low-dose antibiotics


title: A12_low-dose antibiotics


title: A11_low-dose antibiotics


title: A10_low-dose antibiotics


title: brain_malignantglioma_NOA-08_002

description: tumor


title: brain_malignantglioma_NOA-08_004

description: tumor


title: Y_B2_rep1

description:
Dev-B2-1
processed data file: TPM_matrix.txt

tag: age

value: Whole body


title: A9_low-dose antibiotics


title: A8_low-dose antibiotics


title: CGL2_control

description: liquid hybridization capture-based bisulfite sequencing (LHC-BS) approach for library construction

value: control


title: AGL9_low-dose antibiotics


title: CGL1_control


title: Y_B6_rep1

description:
Dev-B6-1
processed data file: TPM_matrix.txt

value: Day 6 of juvenile stage


title: C11_control


title: C12_control


title: C8_control


title: C9_control


title: C10_control


title: CGL6_control


title: CGL7_control


title: C31B (ATAC-Seq)

city: Shanghai

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
The adaptors were cut using Ngmerge
Pair-end reads were aligned to hg38 genome using bowtie2 under default parameters
The open chromation regions were detected by macs2 using the setting of "--nomodel --shift -37 --extsize 73 --keep-dup all -q 0.05 --broad"
Genome_build: hg38
Supplementary_files_format_and_content: broadPeak

source_name: brain prefrontal cortex region tissues

extract_protocol:
Place frozen tissue into a pre-chilled 2 ml Dounce with 2 ml cold nuclei lysis buffer. Allow frozen tissue to thaw for 5 minutes. Dounce with A pestle until resistance goes away ( 10 strokes). Dounce with B pestle for 20 strokes. Pre-clear larger chunks by pelleting at 100 RCF for 1 min in a pre-chilled centrifuge.Count nuclei using Trypan blue staining and aliquot nuclei for ATAC reaction. Harvest and count cells (counting protocol to be de_ned by the user; see APPENDIX3F). Cells should be intact and in a homogenous, single-cell suspension; Centrifuge 50,000 cells 5 min at 500 x g, 4?C. The number of cells at this step is crucial, as the transposase-to-cell ratio determines the distribution of DNA fragments generated. Remove and discard supernatant. Wash cells once with 50 ?l of cold PBS bu_er. Centrifuge 5 min at 500x g, 4?C. Remove and discard supernatant. Gently pipet up and down to resuspend the cell pellet in 50 ?l of cold lysis bu_er. Centrifuge immediately for 10 min at 500 xg, 44?C. Discard the supernatant, and immediately continue to transposition reaction. Make sure the cell pellet is set on ice. To make the transposition reaction mix, combine the following: TD (2x reaction bu_er from Nextera kit) 25 ?l; TDE1 (Nextera Tn5 Transposase from Nextera kit) 2.5 ?l; Nuclease-free H2O 22.5 ?l. Resuspend nuclei pellet (from step 5) in the transposition reaction mix. Incubate the transposition reaction at 37?C for 30 min. Gentle mixing may increase fragment yield. Immediately following transposition, purify using a Qiagen MinElute PCR Puri_cation Kit. Elute transposed DNA in 10 ?l Elution Bu_er (Bu_er EB from the MinElute kit consisting of 10 mM Tris?Cl, pH 8). To amplify transposed DNA fragments, combine the transposed DNA (10 ?l), nuclease-free H2O (10 ?l),25 ?M PCR Primer 1 (2.5 ?l), 25 ?M Barcoded PCR Primer 2 (2.5 ?l), NEBNext High-Fidelity 2x PCR Master Mix (2 5 ?l). Thermal cycle as follows 72?C,5 min, 1 cycle; 98?C,30 sec; 98?C, 10 sec 5 cycles; 63?C, 30 sec; 2?C, 2 min; 4?C.
The library is constructed under the protocol of Iillumina

tag: disease state

value: normal

value: male

value: brain prefrontal cortex region tissues


title: A4_low-dose antibiotics


title: A7_low-dose antibiotics


title: A2_low-dose antibiotics


title: A6_low-dose antibiotics


title: A3_low-dose antibiotics


title: A1_low-dose antibiotics


title: A5_low-dose antibiotics


title: C16_control


title: C13B (ATAC-Seq)


title: C13 (ATAC-Seq)


title: C31 (ATAC-Seq)


title: C25 (ATAC-Seq)


title: aD18 (ATAC-Seq)

value: AD


title: aD7 (ATAC-Seq)


title: aD21 (ATAC-Seq)


title: C23B (ATAC-Seq)


title: C13_control


title: C15_control


title: C14_control


title: AGL3_low-dose antibiotics


title: C7_control


title: C5_control


title: AGL7_low-dose antibiotics


title: C2_control


title: aD16 (ATAC-Seq)


title: C4_control


title: C3_control


title: C6_control


title: aD11 (ATAC-Seq)


title: C1_control


title: AGL12_low-dose antibiotics


title: c13-thra1 (ChIP-seq)

data_processing:
The adaptors were cut using Ngmerge
Pair-end reads were aligned to hg38 genome using bowtie2 under default parameter setting
The TF binding sites were detected by macs2
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
Chromatin was sonicated by Bioruptor (Diagenode, Belgium) under the condition as follows: 20 cycles of 30 s on, 60 s off. The sonicated chromatin was spun down at 12,000 rpm for 10 min at 4 °C to collect the chromatin. Add antibody (10 μg) to the soluble chromatin (80 μg), and incubate at 4 °C with rotation overnight. Protein A/G Dynabeads (10 μl of beads per 1 μg of antibody, Life Tech, 10004D) were washed three times with Low Salt Wash Buffer. The washed Dynabeads were added to the soluble chromatin and antibodies, incubated at 4°C for 4 h with rotation. The magnetic Dynabeads were pelleted by placing the tubes in a magnetic rack and were sequentially washed once with Low Salt Wash Buffer, once with High-salt Wash Buffer, once with LiCl Wash Buffer. Wash the beads three times with TE buffer. Remove any supernatant remaining after the last washing. The beads were resuspended in 150 μl of Elution Buffer (50 mM Tris•Cl pH 8.0, 10 mM EDTA, 1% SDS), followed by incubation for 15 min at 65 °C. Repeat step 7 again, combine the elution, then you have 300 μl of the eluted DNA solution. Add 1 μl of high concentration RNase A (10 mg/ml) to the eluted DNA solution and the Input samples (500 μl), respectively. Incubate them at 37 ℃ for 1 h. Reverse formaldehyde crosslinks by respectively adding 12.5 μl or 55 μl of 5 M NaCl to the eluted DNA solution and the Input samples to a final concentration of 0.2 M. Incubate samples at 65 ℃ (650 rpm) for more than 8 h (less than 16 h).  Add both 80.5 μl of ddH2O and 5 μl of 20 mg/ml Proteinase K to the eluted DNA solution, and just 5 μl of Proteinase K to the Inputs. Incubate at 56 ℃ for 2 h. Extract once with 400 μl of phenol/chloroform/isoamyl alcohol, and once with 400 μl of chloroform/isoamyl alcohol (optional). Transfer 355 μl of supernatant to a new tube. Add 55 μl or 40 μl of 3 M NaAc (pH 5.2, 0.3 M final) to the Input samples and eluted DNA solution, 5 μl of glycogen each sample and mix well. Add 800 μl (two-fold volume) of absolute ethanol. Precipitate at -20 ℃ overnight or at -80 ℃ for 4 h. Centrifuge at 14000 rmp for 20 min at 4 ℃. Wash once with 75% ethanol and store at -20 ℃.
The library is constructed under the protocol of Iillumina

tag: braak

tag: chip antibody

value: THRA (SantaCruz, catalog# SC-56873, lot# J1614)


title: c31-thra1 (ChIP-seq)


title: aD2 (ATAC-Seq)


title: ad1-thra1 (ChIP-seq)


title: ad11-thra1 (ChIP-seq)


title: 20180807-thra1 (ChIP-seq)


title: ad7-thra1 (ChIP-seq)


title: 2018006-olig2 (ChIP-seq)

value: Olig2 (RnD, catalog# AF2418, lot# UPA0718031)


title: c23-thra1 (ChIP-seq)


title: Cellular RNA 3

city: KUALA LUMPUR

first: NADIAH

last: ABU

state: KUALA LUMPUR

address: UKM Medical Molecular Biology, UMBI, UKM MEDICAL CENTER

country: Malaysia

institute: UKM MEDICAL MOLECULAR BIOLOGY INSTITUTE (UMBI)

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.  After washing, slides were scanned with the Agilent Scanner G2505C.  After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test.

source_name: drug-resistant HCT116_cellular RNA

label_protocol: Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HCT116 cells were maintained in RPMI1640 medium supplemented with 10% FBS. All the cells were incubated in a 37 humifidified CO2 chamber equipped with 5%CO2.

extract_protocol: Total cellular RNA was extracted using the Rneasy Kit, and the exosomal RNA was extracted using the Exoeasy Maxi Kit.

treatment_protocol: The cells

tag: cell line

tag: cell type

value: Colorectal Cancer cells

tag: phenotype

value: Drug resistant

tag: molecule subtype

value: cellular RNA


title: ad16-thra1 (ChIP-seq)


title: 2017039-olig2 (ChIP-seq)


title: 2017025-olig2 (ChIP-seq)


title: 2017011-olig2 (ChIP-seq)


title: 2018001-olig2 (ChIP-seq)


title: 2016029-olig2 (ChIP-seq)


title: 20138-olig2 (ChIP-seq)


title: Cellular RNA 1


title: Exosomal RNA 1

source_name: drug-resistant HCT116_exosomal RNA

value: exosomal RNA


title: 2017014-olig2 (ChIP-seq)


title: 20134-olig2 (ChIP-seq)


title: 2018006-atf4 (ChIP-seq)

value: ATF4 (CTS, catalog# 11815S, lot# 4)


title: 2018001-atf4 (ChIP-seq)


title: 2017039-atf4 (ChIP-seq)


title: 201704-atf4 (ChIP-seq)


title: Cellular RNA 2


title: Exosomal RNA 3


title: Hep3B_HES5wt_noDox_rep3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description:
HES5wt_neg_3
Hep3B infected with pTRIPZ expressing HES5wt.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Clariom D Human from Thermo Fisher. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The raw fluorescence intensity values were normalized applying quantile normalization, Kernel Surface background correction and Medianpolish Probeset Summary.

label: Biotin

source_name: Hep3B-HES5 without Dox 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Hep3B cells were cultured in Minimum Essential Medium (MEM) supplemented with 10% fetal calf serum and 1% Penicillin-streptomycin (100 IU/ml and 100 g/ml, respectively).

extract_protocol: Total RNA was extracted from cells with NucleoSpin RNA Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol.

treatment_protocol: HES5wt or HES5-R31G protein expression was induced with 2 µg/ml doxycycline.

value: cell line

tag: infection

value: pTRIPZ expressing HES5wt

tag: doxycycline

value: no


title: 2017025-atf4 (ChIP-seq)

value: female


title: 2017014-atf4 (ChIP-seq)


title: 2017011-atf4 (ChIP-seq)


title: 2017001-atf4 (ChIP-seq)


title: Hep3B_HES5wt_noDox_rep4

description:
HES5wt_neg_4
Hep3B infected with pTRIPZ expressing HES5wt.


title: Hep3B_HES5-R31G_noDox_rep2

description:
HES5mut_neg_2
Hep3B infected with pTRIPZ expressing HES5-R31G.

source_name: Hep3B-HES5-R31G without Dox 48h

value: pTRIPZ expressing HES5-R31G


title: 2016018-olig2 (ChIP-seq)


title: Hep3B_HES5wt_Dox_rep2

description:
HES5wt_pos_2
Hep3B infected with pTRIPZ expressing HES5wt.

source_name: Hep3B-HES5 with Dox 48h

value: yes


title: Exosomal RNA 2


title: 2016029-atf4 (ChIP-seq)


title: Hep3B_HES5wt_noDox_rep2

description:
HES5wt_neg_2
Hep3B infected with pTRIPZ expressing HES5wt.


title: Hep3B_HES5-R31G_noDox_rep3

description:
HES5mut_neg_3
Hep3B infected with pTRIPZ expressing HES5-R31G.


title: Hep3B_HES5-R31G_noDox_rep4

description:
HES5mut_neg_4
Hep3B infected with pTRIPZ expressing HES5-R31G.


title: Hep3B_HES5-R31G_Dox_rep3

description:
HES5mut_pos_3
Hep3B infected with pTRIPZ expressing HES5-R31G.

source_name: Hep3B-HES5-R31G with Dox 48h


title: Hep3B_HES5wt_noDox_rep1

description:
HES5wt_neg_1
Hep3B infected with pTRIPZ expressing HES5wt.


title: Hep3B_HES5wt_Dox_rep3

description:
HES5wt_pos_3
Hep3B infected with pTRIPZ expressing HES5wt.


title: Hep3B_HES5-R31G_Dox_rep1

description:
HES5mut_pos_1
Hep3B infected with pTRIPZ expressing HES5-R31G.


title: Hep3B_HES5-R31G_noDox_rep1

description:
HES5mut_neg_1
Hep3B infected with pTRIPZ expressing HES5-R31G.


title: Hep3B_HES5-R31G_Dox_rep4

description:
HES5mut_pos_4
Hep3B infected with pTRIPZ expressing HES5-R31G.


title: Hep3B_HES5-R31G_Dox_rep2

description:
HES5mut_pos_2
Hep3B infected with pTRIPZ expressing HES5-R31G.


title: Hep3B_HES5wt_Dox_rep1

description:
HES5wt_pos_1
Hep3B infected with pTRIPZ expressing HES5wt.


title: 2016018-atf4 (ChIP-seq)


title: Hep3B_HES5wt_Dox_rep4

description:
HES5wt_pos_4
Hep3B infected with pTRIPZ expressing HES5wt.


title: Hep3B_noDox_rep4

description:
Dox_neg_4
Hep3B control cells.

source_name: Hep3B without Dox 48h


title: Hep3B_noDox_rep2

description:
Dox_neg_2
Hep3B control cells.


title: 20138-atf4 (ChIP-seq)


title: Hep3B_noDox_rep3

description:
Dox_neg_3
Hep3B control cells.


title: 20134-atf4 (ChIP-seq)

value: normal


title: Hep3B_noDox_rep1

description:
Dox_neg_1
Hep3B control cells.


title: Hep3B_Dox_rep4

description:
Dox_pos_4
Hep3B control cells.

source_name: Hep3B with Dox 48h


title: Donor No.8 EC 6h

status: Public on Oct 30 2019

city: Omaha

first: Ahmed

middle: M

last: Abdellatif

state: NE

address: 42 and Emile

department: Surgery-Transplant

institute: University of Nebraska Medical Center

data_processing:
Short raw sequence reads were downloaded from the HiSeq2500 server in FASTQ format and individually mapped to the human reference genome (hg38) using TopHat.
The complete bioinformatics analysis pipeline for the RNAseq data was performed using the Tuxedo protocol, which includes TopHat, Cufflinks, Cuffmerge, and Cuffdiff.
Differential gene expression analysis results from the Cufflinks analysis of individual samples were reported as Fragments Per Kilobase of transcript per Million Mapped reads (FPKM) which reports the normalized expression values for a given gene and accounts for multiple reads for an individual fragment.
Transcripts up- and downregulated relative to controls were considered significantly changed only when the false discovery rate (FDR) adjusted p-value (q-value) was less than 0.05.
Relative differences in gene expression were assessed by comparing the log2 fold change values between the islet FPKMs for bacteria-treated and time-matched controls. For easier interpretation of obtained datasets, all log2 fold change values were converted to their equivalent numeric values.
Genome_build: hg38

source_name: Pacreatic islets

growth_protocol: Bacteroides dorei (BD, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Cat# 17855), Escherichia coli (EC, Invitrogen Cat# 18258012), and Ruminococcus gnavus (RG, ATCC, Cat# 29149) were purchased from commercial vendors and grown according to standard protocols. Both BD and RG were grown anaerobically in tryptic soy broth supplemented with Oxyrase (Oxyrase Inc.) and resazurin salt (Sigma-Aldrich) while EC was grown aerobically in Luria-Bertani broth. All bacteria were allowed to reach early/mid-stationary phase of growth. At the end of culture, bacteria were fixed in 4% paraformaldehyde (PFA) for 30 minutes, rinsed 3 times with sterile PBS and then reconstituted in sterile physiological saline. To ensure all bacteria were killed, bacterial stocks were used to inoculate additional broth. Absence of bacterial growth 48h after inoculation under standard culturing conditions indicated all bacteria were killed by the PFA exposure. For confirmation of the purity of tested bacteria, genomic sequencing was performed for each bacterial strain

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Minikits (Qiagen) according to the manufacturer's recommendations. Next, RNA integrity and concentration were assessed using an Agilent Bioanalyzer 2100 (Agilent) and Nanodrop Spectrophotometer respectively.
cDNA libraries were generated using a SciClone NGS Library Production Robot (Perkin Elmer) and library quality was verified using the Agilent Bioanalyzer.
RNA sequencing was subsequently performed using an Illumina HiSeq2500 system (Illumina, San Diego, CA, USA) to achieve single 100 base pair reads with a read depths of 15-20 million reads per sample.

treatment_protocol: Upon arrival, islets were initially incubated for 6-24h at 37°C in CMRL-1066 medium (Gibco, USA) supplemented with 2mM l-glutamine, 1% penicillin-streptomycin, and 10% fetal bovine serum (FBS).  After that, individual donor islets were cultured in four-well plates containing FBS-free media at 1000 islet equivalents (IEQs) per well. Each well was exposed to one of the three bacterial strains at 10 bacteria per cell (BpC) for 6h or 24h. Time matched controls were also included using IL-1βb  (InvivoGen) at 1ng/ml (positive control) and FBS-free media (negative control).

tag: agent

value: Escherichia coli (EC)

tag: time point


title: Donor No.8 IL-1B 24h


title: Donor No.8 RG 6h

value: Ruminococcus gnavus (RG)


title: Donor No.8 IL-1B 6h


title: Hep3B_Dox_rep3

description:
Dox_pos_3
Hep3B control cells.


title: Donor No.8 RG 24h


title: Donor No.8 SFC 24h

value: Serum-Free Control


title: Donor No.8 BD 24h

value: Bacteroides dorei (BD)


title: Donor No.7 RG 6h


title: Donor No.8 EC 24h


title: Donor No.7 RG 24h


title: Donor No.7 BD 6h


title: Donor No.7 EC 6h


title: Hep3B_Dox_rep2

description:
Dox_pos_2
Hep3B control cells.


title: Donor No.7 EC 24h


title: Donor  No.6 RG 24h


title: Donor  No.6 RG 6h


title: Donor  No.6 EC 6h


title: Donor  No.6 IL-1B 24h


title: Donor  No.6 EC 24h


title: Donor  No.6 IL-1B 6h


title: Donor  No.6 BD 6h


title: Donor  No.6 SFC 24h


title: Donor No.8 BD 6h


title: Donor No.7 SFC 24h


title: Donor No.6 BD 24h


title: Donor No.5 IL-1B 6h


title: Donor No.5 IL-1B 24h


title: Hep3B_Dox_rep1

description:
Dox_pos_1
Hep3B control cells.


title: Donor No.5 RG 24h


title: Donor No.5 EC 24h


title: Donor No.5 BD 6h


title: Donor No.5 BD 24h


title: Donor No.2 SFC 24h


title: Donor No.5 SFC 24h


title: Donor No.2 IL-1B 6h


title: Donor No.2 EC 6h


status: Public on Oct 27 2019

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
Lung_IC_rep2
XL152526_lung_IC_IGO_08742_D_11_S2
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo/+ mice, normal lung, biological rep 2

data_processing:
The first 7 bases were removed from the beginning of reads and appended to the original read names
The 3’ adaptor (5’-GTGTCAGTCACTTCCAGCGGGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’) and bases with Phred quality score lower than 20 were trimmed from reads using cutadapt v1.15 or v1.17. After trimming, reads shorter than 18 nt were discarded.
For HEAP mRNA and input control libraries, processed reads were aligned to the UCSC mm10 mouse genome using STAR (version 2.5.3a). For HEAP miRNA libraries, processed small RNA reads were aligned to a miRNA genome index built from 1,915 murine pre-miRNA sequences from miRbase version 21 (ftp://mirbase.org/pub/mirbase/21/) using Bowtie (version 2.3.4), and these reads were considered true miRNA counts if they fell within plus or minus 4 bps at each of the 5’ and 3’ end of the annotated mature miRNAs.
Reads mapped to the same locus with identical barcodes were considered PCR duplicates and therefore collapsed. This was achieved by storing aligned reads using chromosome names, strand information, positions of the first bases and the 7 nt barcodes as keywords. Representative reads of these unique events were written into a BAM file.
Peaks were called using CLIPanalyze (https://bitbucket.org/leslielab/clipanalyze) from HEAP mRNA libraries using input control libraries as background signals.
Genome_build: mm10
Supplementary_files_format_and_content: csv files of peaks identified in each context and (for HEAP miRNA libraries) miRNA quantifications

source_name: Normal lung from Ago2Halo/+ mice

growth_protocol: Mice were bred and housed in the pathogen-free animal facility at Memorial Sloan-Kettering Cancer Center and were used in accordance with institutional guidelines. Mouse experiments were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center.

extract_protocol:
For HEAP mRNA and miRNA libraries, RNAs were isolated along with the HaloTag-Ago2 fusion protein using HaloTag ligands conjugated to sepharose beads. RNAs were extracted from sepharose beads using phenol/chloroform. For input control libraries, RNAs were extracted from whole-cell lysates after RNAse A treatment using DynaBeads MyOne Silane.
RNAs were ligated to RNA adaptors on both ends (3' RNA adaptor RL3: GUGUCAGUCACUUCCAGCGG; 5' RNA adaptor RL5D-6N: AGGGAGGACGAUGCGGNNNNNNG). After reverse transcription with a DNA primer DP3 (CCGCTGGAAGTGACTGACAC), the library was amplified with DNA primers DP3 and DP5 (AGGGAGGACGATGCGG). Illumina sequencing adaptors, sequencing primer binding sites and Illumina Truseq indexes for library multiplexing were introduced to the amplified libraries by PCR using primers DP3-barcode (CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCCCGCTGGAAGTGACTGACAC) and DSFP5 (AATGATACGGCGACCACCGACTATGGATACTTAGTCAGGGAGGACGATGCGG). After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were run on a HiSeq 2500 in Rapid Mode in a 125/100bp single end run, using the HiSeq Rapid SBS Kit v2 (Illumina). Sequencing primers used were custom SSP1 primer (CTATGGATACTTAGTCAGGGAGGACGATGCGG) and the Illumina index read SP2 primer.

treatment_protocol: Ago2Halo/+ mice were crossed to mice heterozygous knockout for the miR-17~92 locus to generate Ago2Halo/+; miR-17~92+/- mice. E13.5 embryos of genotypes Ago2Halo/+; miR-17~92+/+, Ago2Halo/+; miR-17~92+/- and Ago2Halo/+; miR-17~92-/- were obtained by timed-mating between Ago2Halo/+; miR-17~92+/- and miR-17~92+/- mice. For the generation of libraries from P13 cortex, cortices were harvested from Ago2Halo/+ mice at postnatal day 13. For the generation of Bcan-Ntrk1-driven gliomas, a 1:1 mixture of Ad-BN and Ad-Cre was administrated to Ago2Halo-LSL/+; p53fl/fl mice (4~6 weeks old), via stereotactic intracranial injection. Gliomas were harvested around 80 days after injection. Normal cortices were harvested from age-matched Ago2Halo/+ mice. For the generation of Eml4-Alk-driven lung adenocarcinomas, 10~12-week-old Ago2Halo-LSL/+ mice were intratracheally infected with a 1:1 mixture of Ad-EA and Ad-Cre. To generate the KRas-G12D; p53-null lung tumors, 10~12-week-old Ago2Halo-LSL/+; KRasLSL  -G12D/+; p53fl/fl mice were infected with Ad-Cre. Lung tumors were harvested around 3 months after infection. Normal lung tissues were obtained from age-matched Ago2Halo/+ mice.

tag: strain background

tag: genotype/variation

tag: tissue

value: Normal lung

tag: molecule/library type

value: input control


title: Donor No.1 SFC 24h


title: Donor No.1 EC 6h


title: Donor No.5 RG 6h


title: input control library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null NSCLCs, biological rep 2

description:
10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2
KP_NSCLC_IC_rep2
PAGE_IC_2_IGO_08133_D_11_S15
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 2

source_name: KRasG12D; p53-null lung adenocarcinomas from Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice

value: KRasG12D; p53-null lung adenocarcinomas


title: input control library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null NSCLCs, biological rep 1

description:
10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2
KP_NSCLC_IC_rep1
PAGE_IC_1_IGO_08133_D_12_S14
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 1


description:
Lung_IC_rep1
PAGE_IC_6_IGO_08133_D_2_S7
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo/+ mice, normal lung, biological rep 1


description:
Lung_miRNA_rep2
XL152526_lung_miRNA_IGO_08742_D_17_S10
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo/+ mice, normal lung, biological rep 2

value: miRNA


title: Donor No.1 IL-1B 6h


description:
Lung_miRNA_rep1
6-miRNA-5_IGO_08133_D_4_S10
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo/+ mice, normal lung, biological rep 1


title: Donor No.5 EC 6h


title: input control library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 1

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_IC_rep1
PAGE_IC_3_IGO_08133_D_6_S1
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 1

source_name: Eml4-Alk lung adenocarcinoma from Ago2Halo-LSL/+ mice

value: Eml4-Alk lung adenocarcinoma


title: input control library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 3

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_IC_rep3
PAGE_IC_7_IGO_08133_D_10_S5
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 3


title: Donor No.7 BD 24h


title: HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 2

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_miRNA_rep2
4-miRNA-5_IGO_08133_D_7_S9
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 2


title: HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 1

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_miRNA_rep1
3-miRNA-5_IGO_08133_D_8_S12
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 1


title: HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 3, technical rep 2

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_miRNA_rep3_2
6_miRNA_IGO_08133_C_8_S9
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 3, technical rep 2


title: HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 3, technical rep 1

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_miRNA_rep3_1
6_miRNA_IGO_08133_C_8_S4
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 3, technical rep 1


title: HEAP miRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null NSCLCs, biological rep 2

description:
10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2
KP_NSCLC_miRNA_rep2
2-miRNA-5_IGO_08133_D_13_S4
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 2


title: HEAP miRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null NSCLCs, biological rep 1

description:
10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2
KP_NSCLC_miRNA_rep1
1-miRNA-5_IGO_08133_D_14_S11
processed data file: lung_tumor_mirna_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 1


description:
Lung_mRNA_rep2
XL152526_lung_HEAP_IGO_08742_D_5_S5
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo/+ mice, normal lung, biological rep 2

value: mRNA


description:
Lung_mRNA_rep1
PAGE_mRNA_6_IGO_08133_D_9_S16
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo/+ mice, normal lung, biological rep 1


title: input control library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 2

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_IC_rep2
PAGE_IC_4_IGO_08133_D_5_S6
processed data file: lung_tumor_peaks_all.csv
input control library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 2


title: HEAP mRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 2

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_mRNA_rep2
PAGE_mRNA_4_IGO_08133_D_16_S3
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 2


title: RNA-seq, AgoHalo/+ mice; normal lung, biological rep 3

description:
XL805_IGO_08718_B_3_S12
processed data file: lung_tumor_RNAseq_counts.csv

data_processing:
RNA-seq reads were aligned to the standard mouse genome (mm10) using Hisat2 v0.1.6-beta
Aligned reads were counted at each gene locus using the GENCODE annotation vM22
Differential gene expression analysis was performed using DESeq2 v1.20.0
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing differential gene expression analysis results and gene counts

extract_protocol:
Lung tumors or normal lung tissues were resected from mice and homogenized in TRIzol Reagent. Total RNA were extracted following the manufacturer's instructions, treated with DNase and cleaned up using the Qiagen RNeasy kit.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit.

treatment_protocol: For the generation of Eml4-Alk-driven lung adenocarcinomas, 10~12-week-old Ago2Halo-LSL/+ mice were intratracheally infected with a 1:1 mixture of Ad-EA and Ad-Cre. To generate the KRas-G12D; p53-null lung tumors, 10~12-week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were infected with Ad-Cre. Lung tumors were harvested around 3 months after infection. Normal lung tissues were obtained from age-matched Ago2Halo/+ mice.


title: HEAP mRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null NSCLCs, biological rep 1

description:
10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2
KP_NSCLC_mRNA_rep1
PAGE_mRNA_1_IGO_08133_D_17_S17
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 1


title: HEAP mRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null NSCLCs, biological rep 2

description:
10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2
KP_NSCLC_mRNA_rep2
PAGE_mRNA_2_IGO_08133_D_18_S18
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 2


description:
cortex of postnatal day 13 Ago2Halo/+ mice was used
P13_cortex_IC_rep1
B1_IC_IGO_08916_B_5_S5
processed data file: P13_cortex_peaks.csv
input control library, Ago2Halo/+ P13 mice, cortex, biological rep 1

source_name: cortex from P13 Ago2Halo/+ mice

value: cortex


description:
cortex of postnatal day 13 Ago2Halo/+ mice was used
P13_cortex_mRNA_rep2
P13_B2_IGO_08916_B_2_S10
processed data file: P13_cortex_peaks.csv
HEAP mRNA library, Ago2Halo/+ P13 mice, cortex, biological rep 2


description:
Cortex_IC_rep3
XL1526_cortex_IC_IGO_08742_D_8_S11
processed data file: glioma_cortex_peaks_all.csv
input control library, Ago2Halo/+ mice, cortex, biological rep 3

source_name: cortex from Ago2Halo/+ mice


description:
cortex of postnatal day 13 Ago2Halo/+ mice was used
P13_cortex_mRNA_rep1
P13_B1_IGO_08916_B_1_S9
processed data file: P13_cortex_peaks.csv
HEAP mRNA library, Ago2Halo/+ P13 mice, cortex, biological rep 1


title: RNA-seq, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 3

description:
XL1087_IGO_08718_B_10_S8
processed data file: lung_tumor_RNAseq_counts.csv

tag: treatment

value: 10~12 week-old Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice were intratracheally infected with Ad-Cre to induce KRasG12D; p53-null tumors and activate Halo-Ago2


title: RNA-seq, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 2

description:
XL1078_1142_IGO_08718_B_9_S18
processed data file: lung_tumor_RNAseq_counts.csv


title: RNA-seq, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 4

description:
XL1089_IGO_08718_B_11_S9
processed data file: lung_tumor_RNAseq_counts.csv


description:
Cortex_IC_rep1
4-IC_IGO_08742_B_10_S7
processed data file: glioma_cortex_peaks_all.csv
input control library, Ago2Halo/+ mice, cortex, biological rep 1


description:
Cortex_IC_rep2
XL1525_cortex_IC_IGO_08742_D_7_S17
processed data file: glioma_cortex_peaks_all.csv
input control library, Ago2Halo/+ mice, cortex, biological rep 2


title: RNA-seq, Ago2Halo-LSL/+; KRasLSL-G12D/+; p53fl/fl mice with KRasG12D; p53-null lung adenocarcinomas, biological rep 1

description:
XL1077_IGO_08718_B_8_S17
processed data file: lung_tumor_RNAseq_counts.csv


title: RNA-seq, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 4

description:
XL989_IGO_08718_B_7_S16
processed data file: lung_tumor_RNAseq_counts.csv

value: 10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_IC_rep1
1-IC_IGO_08742_B_7_S10
processed data file: glioma_cortex_peaks_all.csv
input control library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 1

source_name: Bcan-Ntrk1 gliomas from Ago2Halo-LSL/+; p53fl/fl mice

value: Ago2Halo-LSL/+; p53fl/fl

value: Bcan-Ntrk1 gliomas


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_IC_rep2
2-IC_IGO_08742_B_8_S12
processed data file: glioma_cortex_peaks_all.csv
input control library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 2


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_IC_rep3
XL909_BN_IC_IGO_08742_D_12_S1
processed data file: glioma_cortex_peaks_all.csv
input control library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 3


description:
Cortex_miRNA_rep3
XL1526_cortex_miRNA_IGO_08742_D_14_S16
processed data file: glioma_cortex_miRNA_counts.csv
HEAP miRNA library, Ago2Halo/+ mice, cortex, biological rep 3


title: RNA-seq, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 3

description:
XL822_IGO_08718_B_6_S15
processed data file: lung_tumor_RNAseq_counts.csv


title: HEAP mRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 3

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_mRNA_rep3
6_mRNA_8_IGO_08133_D_1_S13
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 3


title: RNA-seq, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 2

description:
XL770_IGO_08718_B_5_S14
processed data file: lung_tumor_RNAseq_counts.csv


description:
cortex of postnatal day 13 Ago2Halo/+ mice was used
P13_cortex_IC_rep2
B2_IC_IGO_08916_B_6_S6
processed data file: P13_cortex_peaks.csv
input control library, Ago2Halo/+ P13 mice, cortex, biological rep 2


title: HEAP mRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk NSCLCs, biological rep 1

description:
10~12 week-old Ago2Halo-LSL/+ mice were intratracheally infected with Ad-EA and Ad-Cre to induce Eml4-Alk lung adenocarcinomas and activate Halo-Ago2
EA_NSCLC_mRNA_rep1
PAGE_mRNA_3_IGO_08133_D_15_S2
processed data file: lung_tumor_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 1


description:
Cortex_miRNA_rep1
4-miRNA_IGO_08742_B_4_S17
processed data file: glioma_cortex_miRNA_counts.csv
HEAP miRNA library, Ago2Halo/+ mice, cortex, biological rep 1


title: RNA-seq, Ago2Halo-LSL/+ mice with Eml4-Alk lung adenocarcinomas, biological rep 1

description:
2732869_IGO_08718_B_4_S13
processed data file: lung_tumor_RNAseq_counts.csv


title: RNA-seq, AgoHalo/+ mice; normal lung, biological rep 2

description:
XL1261_IGO_08718_B_13_S11
processed data file: lung_tumor_RNAseq_counts.csv


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_miRNA_rep2
2-miRNA_IGO_08742_B_2_S15
processed data file: glioma_cortex_miRNA_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 2


title: RNA-seq, AgoHalo/+ mice; normal lung, biological rep 1

description:
XL1260_IGO_08718_B_12_S10
processed data file: lung_tumor_RNAseq_counts.csv


description:
Cortex_mRNA_rep2
XL1525_cortex_HEAP_IGO_08742_D_1_S8
processed data file: glioma_cortex_peaks_all.csv
HEAP mRNA library, Ago2Halo/+ mice, cortex, biological rep 2


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_miRNA_rep1
1-miRNA_IGO_08742_B_1_S13
processed data file: glioma_cortex_miRNA_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 1


description:
Cortex_mRNA_rep3
XL1526_cortex_HEAP_IGO_08742_D_2_S6
processed data file: glioma_cortex_peaks_all.csv
HEAP mRNA library, Ago2Halo/+ mice, cortex, biological rep 3


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_mRNA_rep2
2-mRNA_IGO_08742_B_14_S2
processed data file: glioma_cortex_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 2


title: HEAP IC library, Ago2Halo/+ E13.5 embryos, het KO for the miR-17~92 cluster, biological rep 1

description:
E13.5_embryo_IC_miR-17~92-HET1
2-Het-IC_IGO_08827_B_18_S14
processed data file: emrbyo_peaks.csv
HEAP IC library, Ago2Halo/+ E13.5 embryos, heterozygous KO for the miR-17~92 cluster, biological rep 1

source_name: Ago2Halo/+; miR-17~92+/- E13.5 embryos

value: E13.5 embryos


title: HEAP IC library, Ago2Halo/+ E13.5 embryos, het KO for the miR-17~92 cluster, biological rep 2

description:
E13.5_embryo_IC_miR-17~92-HET2
4-Het-IC_IGO_08827_B_20_S22
processed data file: emrbyo_peaks.csv
HEAP IC library, Ago2Halo/+ E13.5 embryos, heterozygous KO for the miR-17~92 cluster, biological rep 2


title: HEAP miRNA library, Ago2Halo/+ E13.5 embryos,  KO for the miR-17~92 cluster

description:
E13.5_embryo_miRNA_miR-17~92-KO
1-KO-miRNA_IGO_08827_B_9_S2
processed data file: miR-17~92_E13.5_embryos_mirna_counts.csv
HEAP miRNA library, Ago2Halo/+ E13.5 embryos, homozygous KO for the miR-17~92 cluster

source_name: Ago2Halo/+; miR-17~92-/- E13.5 embryos


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_mRNA_rep1
1-mRNA_IGO_08742_B_13_S1
processed data file: glioma_cortex_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 1


title: HEAP miRNA library, Ago2Halo/+ E13.5 embryos, het KO for the miR-17~92 cluster, biological rep 1

description:
E13.5_embryo_miRNA_miR-17~92-HET1
2-Het-miRNA_IGO_08827_B_10_S9
processed data file: miR-17~92_E13.5_embryos_mirna_counts.csv
HEAP miRNA library, Ago2Halo/+ E13.5 embryos, heterozygous KO for the miR-17~92 cluster, biological rep 1


title: HEAP mRNA library, Ago2Halo/+ E13.5 embryos, het KO for the miR-17~92 cluster, biological rep 1

description:
E13.5_embryo_mRNA_miR-17~92-HET1
2-Het-mRNA_IGO_08827_B_2_S6
processed data file: emrbyo_peaks.csv
HEAP mRNA library, Ago2Halo/+ E13.5 embryos, heterozygous KO for the miR-17~92 cluster, biological rep 1


title: HEAP mRNA library, Ago2Halo/+ E13.5 embryos, het KO for the miR-17~92 cluster, biological rep 2

description:
E13.5_embryo_mRNA_miR-17~92-HET2
4-Het-mRNA_IGO_08827_B_4_S4
processed data file: emrbyo_peaks.csv
HEAP mRNA library, Ago2Halo/+ E13.5 embryos, heterozygous KO for the miR-17~92 cluster, biological rep 2


description:
Cortex_miRNA_rep2
XL1525_cortex_miRNA_IGO_08742_D_13_S18
processed data file: glioma_cortex_miRNA_counts.csv
HEAP miRNA library, Ago2Halo/+ mice, cortex, biological rep 2


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_miRNA_rep3
XL909_BN_miRNA_IGO_08742_D_18_S9
processed data file: glioma_cortex_miRNA_counts.csv
HEAP miRNA library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 3


title: HEAP miRNA library, Ago2Halo/+ E13.5 embryos, WT for the miR-17~92 cluster

description:
E13.5_embryo_miRNA_miR-17~92-WT
3-WT-miRNA_IGO_08827_B_11_S19
processed data file: miR-17~92_E13.5_embryos_mirna_counts.csv
HEAP miRNA library, Ago2Halo/+ E13.5 embryos, wild-type for the miR-17~92 cluster

source_name: Ago2Halo/+; miR-17~92+/+ E13.5 embryos


title: HEAP mRNA library, Ago2Halo/+ E13.5 embryos, WT for the miR-17~92 cluster

description:
E13.5_embryo_mRNA_miR-17~92-WT
3-WT-mRNA_IGO_08827_B_3_S5
processed data file: emrbyo_peaks.csv
HEAP mRNA library, Ago2Halo/+ E13.5 embryos, wild-type for the miR-17~92 cluster


title: siNC-2-Rep8

status: Public on Oct 21 2019

city: Stanford

first: Jesse

last: Engreitz

state: CA

address: 240 Pasteur Drive

institute: Stanford University

data_processing:
Samples demultiplexed using BRBseqTools.1.3 into fastqs annotated in headers with RT barcode + UMI
Trim adaptors with BRBseqTools.1.3
Align to hg19.Refseq.gtf using STAR-2.5.6b
Count UMIs per gene with BRBseqTools.1.3
Genome_build: hg19
Supplementary_files_format_and_content: counts.txt is a tab-delimited file conataining the number of UMIs corresponding to sequencing reads aligning to each gene

source_name: siNC-2, K562 cells

growth_protocol: K562 cells were grown in RPMI with 10% FBS.

extract_protocol:
Ten thousand cells were lysed in RLT and RNA was extracted with 2.2X volume Agencourt RNAClean XP SPRI beads
BRB-Seq Version 2 3' RNA-Seq protocol (see Alpern et al. 2018)

treatment_protocol: 200000 cells were transfected with the listed siRNA and grown for 48 hours

tag: sirna

value: Ambion Silencer Select 4390847

tag: sirna dose

tag: target gene

value: NC


title: Fulco-2018-HIC004

data_processing:
Library strategy: HiC-Seq
The paired end reads were aligned separately using BWA against the mm9 mouse build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

source_name: mouse ES cells

growth_protocol: 2i media conditions

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols

treatment_protocol: treatment protocol for specific samples are specified in the SAMPLES section

value: V6.5 mES cells

tag: protocol

value: in situ Hi-C


title: siNC-2-Rep7

tag: cell line


description:
Cortex_mRNA_rep1
4-mRNA_IGO_08742_B_16_S4
processed data file: glioma_cortex_peaks_all.csv
HEAP mRNA library, Ago2Halo/+ mice, cortex, biological rep 1


title: Fulco-2018-HIC001


description:
4~6 week-old Ago2Halo-LSL/+; p53fl/fl mice were intracranially co-infected with Ad-BN and Ad-Cre to induce Bcan-Ntrk1 glioma and activate Halo-Ago2. Gliomas were harvested ~80 days post infection.
Bcan-Ntrk1_gliomas_mRNA_rep3
XL909_BN_HEAP_IGO_08742_D_6_S15
processed data file: glioma_cortex_peaks_all.csv
HEAP mRNA library, Ago2Halo-LSL/+; p53fl/fl mice with Bcan-Ntrk1 glioma, biological rep 3


title: siNC-2-Rep4

value: 25 nM


title: HEAP mRNA library, Ago2Halo/+ E13.5 embryos,  KO for the miR-17~92 cluster

description:
E13.5_embryo_mRNA_miR-17~92-KO
1-KO-mRNA_IGO_08827_B_1_S1
processed data file: emrbyo_peaks.csv
HEAP mRNA library, Ago2Halo/+ E13.5 embryos, homozygous KO for the miR-17~92 cluster


title: siNC-2-Rep2


title: Fulco-2018-HIC003


title: siNC-2-Rep6


title: siNC-2-Rep5


title: HEAP IC library, Ago2Halo/+ E13.5 embryos,  KO for the miR-17~92 cluster

description:
E13.5_embryo_IC_miR-17~92-KO
1-KO-IC_IGO_08827_B_17_S15
processed data file: emrbyo_peaks.csv
HEAP IC library, Ago2Halo/+ E13.5 embryos, homozygous KO for the miR-17~92 cluster


title: HEAP miRNA library, Ago2Halo/+ E13.5 embryos, het KO for the miR-17~92 cluster, biological rep 2

description:
E13.5_embryo_miRNA_miR-17~92-HET2
4-Het-miRNA_IGO_08827_B_12_S18
processed data file: miR-17~92_E13.5_embryos_mirna_counts.csv
HEAP miRNA library, Ago2Halo/+ E13.5 embryos, heterozygous KO for the miR-17~92 cluster, biological rep 2


title: siNC-1-Rep8

source_name: siNC-1, K562 cells

value: Ambion Silencer Select 4390844


title: siNC-1-Rep6


title: HEAP IC library, Ago2Halo/+ E13.5 embryos, WT for the miR-17~92 cluster

description:
E13.5_embryo_IC_miR-17~92-WT
3-WT-IC_IGO_08827_B_19_S13
processed data file: emrbyo_peaks.csv
HEAP IC library, Ago2Halo/+ E13.5 embryos, wild-type for the miR-17~92 cluster

value: input control


title: siNC-1-Rep7


title: siNC-1-Rep5


title: siNC-2-Rep1


title: siNC-1-Rep4


title: siNC-1-Rep2


title: siNC-1-Rep3


title: siNC-1-Rep1


title: siGATA1-2-Rep4

source_name: siGATA1-2, K562 cells

value: Ambion Silencer Select s5594


title: Fulco-2018-HIC002


title: siGATA1-2-Rep3


title: siNC-2-Rep3


title: siGATA1-2-Rep2


title: siGATA1-2-Rep1


title: siGATA1-1-Rep3

source_name: siGATA1-1, K562 cells

value: Ambion Silencer Select s5593


title: siGATA1-1-Rep1


title: siGATA1-1-Rep2


title: the largest follicle (F1) rep4

status: Public on Oct 16 2019

city: Chongqing

first: Gao

last: Guangliang

address: Street Address, No. 51 Changlong Avenue Rongchang County

institute: Chongqing Academy of Animal Sciences

description:
domestic goose
4HPGF1

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of six strand-specific libraries were mapped to the pig reference genome (Suscrofa.10.2 from Ensemble) with TopHat (v.2.1.0)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Cufflinks (v.2.2.1).
Cuffquant (part of Cufflinks) was used to generate abundance files, which were applied to Cuffdiff (part of Cufflinks) to detect DE mRNAs/genes between the two groups.
Transcripts were assembled by Stringtie version 1.2.2.
AssemblyLine (http://assemblyline.googlecode.com) was used to characterize and filter background noise and to perform meta-assembly by merging the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
To obtain genomic characterizations for all identified lncRNA transcripts, we ran FEELnc_classifier.pl (a Perl script in FEELnc).
Genome_build: Goose
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Anser cygnoides

source_name: goose granulosa cells

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: development stage

value: goose granulosa cells

tag: age

value: 40 Week


title: siGATA1-1-Rep4


title: the largest follicle (F1) rep3

description:
domestic goose
3HPGF1


title: the largest follicle (F1) rep5

description:
domestic goose
5HPGF1


title: the second largest follicle (F2) rep4

description:
domestic goose
4HPGF2


title: the second largest follicle (F2) rep2

description:
domestic goose
2HPGF2


title: the largest follicle (F1) rep1

description:
domestic goose
1HPGF1


title: the largest follicle (F1) rep2

description:
domestic goose
2HPGF1


title: the second largest follicle (F2) rep5

description:
domestic goose
5HPGF2


title: the second largest follicle (F2) rep1

description:
domestic goose
1HPGF2


title: the third largest follicle (F3) rep4

description:
domestic goose
4HPGF3


title: the third largest follicle (F3) rep5

description:
domestic goose
5HPGF3


title: the third largest follicle (F3) rep3

description:
domestic goose
3HPGF3


title: the second largest follicle (F2) rep3

description:
domestic goose
3HPGF2


title: the third largest follicle (F3) rep2

description:
domestic goose
2HPGF3


title: the fourth largest follicle (F4) rep2

description:
domestic goose
2HPGF4


title: the fourth largest follicle (F4) rep1

description:
domestic goose
1HPGF4


title: the fifth largest follicle (F5) rep3

description:
domestic goose
3HPGF5


title: the fifth largest follicle (F5) rep4

description:
domestic goose
4HPGF5


title: the fourth largest follicle (F4) rep3

description:
domestic goose
3HPGF4


title: the fourth largest follicle (F4) rep5

description:
domestic goose
5HPGF4


title: the fifth largest follicle (F5) rep2

description:
domestic goose
2HPGF5


title: Large yellow follicle rep3

description:
domestic goose
3HPG8-10

value: LYF


title: Large yellow follicle rep4

description:
domestic goose
4HPG8-10


title: Samll yellow follicle rep5

description:
domestic goose
5HPG6-8

value: SYF


title: Samll yellow follicle rep4

description:
domestic goose
4HPG6-8


title: Large yellow follicle rep2

description:
domestic goose
2HPG8-10


title: Large yellow follicle rep1

description:
domestic goose
1HPG8-10


title: Samll yellow follicle rep2

description:
domestic goose
2HPG6-8


title: Samll yellow follicle rep3

description:
domestic goose
3HPG6-8


title: Samll yellow follicle rep1

description:
domestic goose
1HPG6-8


title: Large white follicle rep5

description:
domestic goose
5HPG4-6

value: LWF


title: the third largest follicle (F3) rep1

description:
domestic goose
1HPGF3